The seasonal and interannual changes in the fish, macroinvertebrates and phycoperiphyton assemblages of the Guarinó River were examined in relation to the physical and chemical environmental changes associated with the hydrological cycle and the El Niño-Niña/Southern Oscillation (ENSO) between 2007 and 2010. Four samplings (in dry and rainy seasons) were performed per year. Environmental variables (temperature, pH, conductivity, turbidity, oxygen, total nitrogen, orthophosphate, depth and flow rate) were measured. The temporal patterns of the taxonomic compositions for the three assemblages and the functional composition of fish and macroinvertebrate assemblages with respect to environmental variables were examined through canonical discriminant analysis, multidimensional scaling and multiple correlations. The presence and abundance of fishes, macroinvertebrates and algae species were regulated by environmental variables associated with extreme hydrological events, which derived from the natural torrential regimen of the basin and larger-scale phenomena, such as El Niño and La Niña. Fish abundance and richness were significantly correlated with algal density and pH, the macroinvertebrate density was negatively related to the flow rate and the richness was positively correlated with algal density. The algae richness was positively correlated with pH and negatively correlated with the flow rate and nitrogen. The algal density was positively correlated with pH and temperature and negatively correlated with river flow. The phycoperiphyton assemblage exhibited more direct responses in its density and richness to the hydrological changes (r(2) = 0·743 and 0·800, respectively). In functional terms, the El Niño phenomenon was defined by a greater abundance of omnivorous and insectivorous fishes, as well as filter feeders, scrapers and macroinvertebrate predators. During La Niña, a greater abundance of benthic fishes (both detritivorous and insectivorous) and shredder and collector-gatherer macroinvertebrates was observed. Differentiated responses recorded in the community were based on adaptive strategies for the local hydrological regime that enable fast recovery under conditions such as ENSO phenomena. Composition changes according to adaptations to different hydrological scenarios and the predominance of generalists' trophic guilds and species with plasticity in their habits and their ranges of environmental tolerance were found, supporting the habitat templet model.